Microbiology_MBIO 302_Chapter-6_2_Mutation.pptx

Microbiology lecture

1. DNA MUTATION

2. A mutation is a permanent change in the nucleotide sequence of DNA. Mutations in genes alter the product of a gene or prevent the gene from functioning properly or completely. For example, when the gene for an enzyme mutates, the enzyme encoded by the gene may become inactive or less active because its amino acid sequence has changed. However, a mutation can be beneficial if, for instance, the altered enzyme encoded by the mutant gene has a new or enhanced activity that benefits the cell. Organism with mutation is called mutant while the organism without mutation is wild type. DNA MUTATION

3. In genetics, a  mutagen  is a physical, chemical or biological agent that permanently changes genetic material, usually DNA, in an organism and thus increases the frequency of mutations above the natural background level. Mutagens that lead to an increased chance of cancer are called carcinogens. Not all mutations are caused by mutagens: so-called "spontaneous mutations" occur due to spontaneous hydrolysis, errors in DNA replication, repair and recombination. 1. Physical mutagens Ionizing radiations such as X-rays, gamma rays and alpha particles cause DNA breakage and other damages. The most common lab sources include cobalt-60 and cesium-137. Ultraviolet radiations with wavelength above 260 nm are absorbed strongly by bases, producing pyrimidine dimers, which can cause error in replication if left uncorrected. Radioactive decay, such as 14C in DNA which decays into nitrogen. 2. Biological mutagens Transposon, a section of DNA that undergoes autonomous fragment relocation/multiplication. Its insertion into chromosomal DNA disrupts functional elements of the genes. Virus – Virus DNA may be inserted into the genome and disrupts genetic function. Infectious agents have been suggested to cause cancer as early as 1911 by Peyton Rous who discovered the Rous sarcoma virus. Bacteria – some bacteria such as Helicobacter pylori cause inflammation during which oxidative species are produced, causing DNA damage and reducing efficiency of DNA repair systems, thereby increasing mutation. 3. Intercalating agents Ethidium bromide and proflavine, are molecules that may insert between bases in DNA, causing frameshift mutation during replication. Some such as daunorubicin may block transcription and replication, making them highly toxic to proliferating cells. Causes of Mutations/Mutagens https://en.wikipedia.org/wiki/Mutagen

4. 4. DNA reactive chemical mutagens: A large number of chemicals may interact directly with DNA. Reactive oxygen species (ROS) – These may be superoxide, hydroxyl radicals and hydrogen peroxide, and large number of these highly reactive species are generated by normal cellular processes, for example as a by-products of mitochondrial electron transport, or lipid peroxidation. These ROS may result in the production of many base adducts, as well as DNA strand breaks and crosslinks. Deaminating agents, for example nitrous acid which can cause transition mutations by converting cytosine to uracil. Polycyclic aromatic hydrocarbon (PAH), when activated to diol-epoxides can bind to DNA and form adducts. Alkylating agents such as ethylnitrosourea . The compounds transfer methyl or ethyl group to bases or the backbone phosphate groups. Guanine when alkylated may be mispaired with thymine. Some may cause DNA crosslinking and breakages. Nitrosamines are an important group of mutagens found in tobacco and may also be formed in smoked meats and fish via the interaction of amines in food with nitrites added as preservatives. Other alkylating agents include mustard gas and vinyl chloride. Psoralen combined with ultraviolet radiation causes DNA cross-linking and hence chromosome breakage. 5. Metals: Arsenic, cadmium, chromium, nickel and their compounds may be mutagenic. Arsenic, chromium, iron, and nickel may be associated with the production of ROS, and some of these may also alter the fidelity of DNA replication. Nickel may also be linked to DNA hypermethylation and histone deacetylation, while some metals such as cobalt, arsenic, nickel and cadmium may also affect DNA repair processes such as DNA mismatch repair, and base and nucleotide excision repair. 6. Base analog , which can substitute for DNA bases during replication and cause transition mutations.

5. Figure: Oxidation of nucleotides makes a mutagen. The nitrous acid emitted into the air by burning fossil fuels oxidizes adenine.

6. Figure: Oxidation of nucleotides makes a mutagen. The nitrous acid emitted into the air by burning fossil fuels oxidizes adenine.

7. Mutations can be classified as to where they occur: 1. Germinal Mutation (inherited): A change or mutation of a sex cell. (egg or sperm), so all body cells inherit that defective DNA. (Germinal mutations can be chromosomal or gene mutations). Example: Haemophilia. A haploid cell is a cell that contains one complete set of chromosomes. Our sex cells are considered haploid and contain 1 complete set of 23 chromosomes. Our autosomal cells are diploid and contain 2 complete sets of 23 chromosomes. Mutations can occur on genes located on sex chromosomes known as sex-linked genes. These genes on either the X chromosome or the Y chromosome determine the genetic characteristics of sex-linked traits. A gene mutation that occurs on the X chromosome can be dominant or recessive. X-linked dominant disorders are expressed in both males and females. X-linked recessive disorders are expressed in males and can be masked in females if the female's second X chromosome is normal. Y chromosome linked disorders are expressed only in males. 2. Somatic Mutation: Somatic cells give rise to all non-germline tissues. Mutations in somatic cells are called somatic mutations. Because they do not occur in cells that give rise to gametes, the mutation is not passed along to the next generation by sexual means. So, s omatic mutations  can arise after fertilization, as the cells are replicating, dividing, and differentiating into their individual cell types. Example: Birth marks, Cancer. These mutation can arise spontaneously (due to an unknown cause) or they may be caused by an environmental factor. Types of Mutations

8. 2. By impact on protein sequence The effect of a mutation on protein sequence depends in part on where in the genome it occurs, especially whether it is in a coding or non-coding region. Mutations in the non-coding regulatory sequences of a gene, such as promoters, enhancers, and silencers, can alter levels of gene expression, but are less likely to alter the protein sequence. Mutations within introns and in regions with no known biological function (e.g. pseudogenes, retrotransposons) are generally neutral, having no effect on phenotype – though intron mutations could alter the protein product if they affect mRNA splicing. Mutations that occur in coding regions of the genome are more likely to alter the protein product, and can be categorized by their effect on amino acid sequence: 1) Frameshift mutation 2) Point mutation or base-substitution mutation

9. Frameshift mutations Insertions and deletions of nucleotides can cause a frameshift mutation. This causes a complete change to the entire amino acid sequence of a protein after the mutation site. This is because of the way the translated mRNA is read by the ribosomes. The mRNA is read in codons, groups of 3 nucleotides. If an additional 1 or 2 nucleotides are added or removed, the sequence is ‘shifted’. The translation machinery cannot know that there has been an error, and still reads the sequence in triplet codons. This means the entire mRNA and resulting protein are completely different. Frameshift mutations almost always result in a long stretch of altered amino acids and the production of an inactive protein from the mutated gene . In most cases, a nonsense codon will eventually be encountered and thereby terminate translation. Example: Huntington’s disease, for example, is a progressive neurological disorder caused by extra bases inserted into a particular gene.

10. 1. Point mutations refer to changes to a single nucleotide (change to only one codon). These usually take place during DNA replication, and their consequences can be benign, or can be devastating. This depends on the location of the mutation. There are 3 types of point mutation: a. Silent mutation b. Missense mutation c. Nonsense mutation

11. a. Silent mutation (neutral mutation) Silent mutation is the change in DNA base sequence that causes no change in the activity of the product encoded by the gene. If a mutation happens in introns (non-coding part of the DNA) it is known as silent mutation. Introns are cut out of mRNA during processing. A mutation can also be silenced due to the redundant nature of the genetic code. In genetic code more than one codon code for the same amino acid. Silent mutations commonly occur when one nucleotide is substituted for another in the DNA, especially at a location corresponding to the third position of the mRNA codon. Because of the degeneracy of the genetic code, the resulting new mutated codon still code for the same amino acid as the original codon. Since the amino acid is same as original one, it does not affect the structure and composition of protein. Silent mutation causes phenotype of bacteria remain similar to that of wild type. For example, if a mutation happens on the third nucleotide of UUU, because which it changes to UUC it will not change the amino acid in the polypeptide that is being produced from this mRNA. This is due to the fact that UUU and UUC code for the amino acid Phenyl alanine.

12. b. Missense mutations Missense mutations refer to the point mutations in which a single base at one point in the DNA sequence is replaced with a different base causing a change to a single amino acid . When the DNA replicates, the result is a substituted base pair. If a base substitution occurs within a gene that codes for a protein, the mRNA transcribed from the gene will carry an incorrect base at that position. When the mRNA is translated into protein, the incorrect base may cause the insertion of an incorrect amino acid in the protein. If the base substitution results in an amino acid substitution in the synthesized protein, this change in the DNA is known as a missense mutation. Even though only one amino acid is affected, the consequences can be deleterious. Example: Sickle Cell Anaemia Hemoglobin is a protein in your red blood cells that carries oxygen to your body's organs and tissues and transports carbon dioxide from your organs and tissues back to your lungs. If a hemoglobin test reveals that your hemoglobin level is lower than normal, it means you have a low red blood cell count (anemia). Sickle-cell anaemia is caused by a point mutation in the protein  haemoglobin . The amino acid glutamic acid is replaced with valine. The properties of these amino acids are sufficiently different, causing changes in the structure of the protein. This causes red blood cells to become  distorted. Therefore, red blood cells don’t move through capillaries well and can restrict blood flow, causing organ damage, and they can no longer efficiently carry oxygen. For example, change of 4th nucleotide from G to C results in change of amino acid from Valine to leucine. Change of a single nucleotide may result in production of a polypeptide which is non-functional.

13. c . Nonsense mutations Nonsense mutations are a special kind of missense mutation where the amino acid change results in the production of a  stop codon  (UAG, UAA or UGA). These codons do not encode for amino acids, and instead encode a signal to the translation machinery that they should  terminate  the process of translation. The process of making a polypeptide chain stops when the translation machinery reaches a stop codon. This  premature stop codon  results in the production of a  truncated  protein, which is usually non-functional. Example: Duchenne muscular dystrophy Duchenne muscular dystrophy is a degenerative disease associated with progressive muscle weakness. The disease is caused by mutations in the  dystrophin  gene, which is important in skeletal muscle cell structure and function. Nonsense mutations in the dystrophin gene result in a non-functional protein, causing the disease.

14. 3. By effect on structure The sequence of a gene can be altered in a number of ways. Gene mutations have varying effects on health depending on where they occur and whether they alter the function of essential proteins. Mutations in the structure of genes can be classified into several types. Chromosomal Mutation –affect a chromosome and therefore many genes (large-scale mutation). Example: Down’s syndrome. Chromosomal mutations are larger scale mutations than point mutations, typically involving segments of entire chromosomes. Chromosome mutations can result in changes in the number of chromosomes in a cell or changes in the structure of a chromosome. These mutations occur as a result of errors in crossing over during meiosis or by mutagens (chemicals such as nitrous acid, radiation such as X-ray and UV light, etc.). There are four types of chromosomal mutations happens in chromosome structure. Mutations that changes DNA content in a chromosome: 1. Deletion: loss of a piece of chromosome 2. Duplication: more than 1 copy of the same gene become the part of a chromosome Mutations that changes DNA orientation in a chromosome: 3. Inversion: reverses direction of part of chromosome (upside down) 4. Translocation: exchange of chromosome pieces between 2 different (non-homologous) chromosomes

15. Example:  1. Cri du Chat Syndrome. This is caused by a deletion in chromosome 5. It is a rare genetic disorder, and the name comes from the French for “cat-like cry”, which refers to the unusual kitten-like cries of affected children. The disease causes developmental delay, problems with the nervous system and behavioral issues. 2. Williams syndrome is caused by the deletion of genetic material from a specific region of chromosome 7. The deleted region includes 26 to 28 genes, and researchers believe that a loss of several of these genes probably contributes to the characteristic features of this disorder. Deletion: loss of a piece of chromosome Chromosomal deletions involve the loss of an entire region of a chromosome and all the genes contained within it. All the codon will be read incorrectly due to the loss of nucleotides. This causes genes to be lost in the fetus.

16. 2. Duplication: more than 1 copy of the same gene become the part of a chromosome Chromosomal duplications involve the repetition of a region of the chromosome, resulting in double the number of genes (and gene products) which are contained within it. This occurs in some rare genetic disorders and is associated with some cancers.

17. 3. Inversion: reverses direction of part of chromosome (upside down) Chromosomal inversions occur when a particular sequence of nucleotides of chromosome is flipped and reinserted, meaning the sequence is in the opposite orientation. This occurs when the same chromosome breaks and rearranges its sequence.

18. Example: 1. Down syndrome (a part of chromosome #21 becomes attached to another chromosome (#’s 12, 14, 15, or 22). 2. Philadelphia chromosome (chronic myeloid leukaemia or cancer of the blood), where two segments of chromosome 9 and chromosome 22 swap places. This results in a gene fusion that encodes a hybrid protein that is always ‘on’, meaning it is overactive. The resulting protein contains a region or domain capable of stimulating cell division, but no longer requires to be activated by other cell signals. As it is constantly switched on, continuously stimulating cell division resulting in a loss of the ability to regulate cellular growth. This contributes to cancer by allowing the cell to divide uncontrollably. 4. Translocation: exchange of chromosome pieces between 2 different (non-homologous) chromosomes Chromosomal translocations occur when a part of one chromosome is incorrectly fused to a segment of another chromosome. The danger of these types of mutations is the possibility for gene fusions.

19. Gene Mutation Chromosomal Mutation Definition An alteration of the nucleotide sequence of a gene Alterations in the chromosome structure or chromosome number Cause Errors in DNA replication and mutagens such as UV and chemicals cause gene mutations. Errors in crossing over during meiosis cause chromosomal mutations. Types Point mutations (silent, nonsense and missense) and frameshift mutation Deletion, Duplication, Inversion and Translocation mutation Number of Genes Affected A single gene is affected by a gene mutation. Several genes are affected by a chromosomal mutation. Influence The influence of gene mutation is comparatively low. Chromosomal mutations can sometimes be lethal. Disease Sickle cell anemia, hemophilia, cystic fibrosis, Huntington syndrome, Tay-Sachs disease, and cancers are caused by gene mutations. Klinefelter syndrome, Turner syndrome, and Down syndrome are caused by chromosomal mutations. Difference between Gene mutation and Chromosomal mutation

20. http://www2.csudh.edu/nsturm/CHEMXL153/DNAMutationRepair.htm#:~:text=There%20are%20three%20types%20of,base%20substitutions%2C%20deletions%20and%20insertions.&text=Single%20base%20substitutions%20are%20called,which%20causes%20sickle%2Dcell%20disease . https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book%3A_Introductory_Biology_(CK-12)/04%3A_Molecular_Biology/4.08%3A_Mutation_Types https://pt.slideshare.net/CSKAZIPYO/gene-mutation-and-its-types/10 https://en.wikipedia.org/wiki/Mutation https://biocyclopedia.com/index/genetics/mutations_molecular_level_mechanism/effect_of_radiations_on_nucleotide_sequence.php https://www.chegg.com/homework-help/questions-and-answers/mutations-possible-10-points-added-class-activities-online-canvas-assignments-category-giv-q37342075